Merge github.com:genenetwork/genenetwork2 into acenteno

2 files changed, 284 insertions, 0 deletions

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
new file mode 100755
index 00000000..08652454
--- /dev/null
+++ b/scripts/authentication/group.py
@@ -0,0 +1,178 @@
+#!/usr/bin/env python3
+"""A script for adding users to a specific group.
+
+Example:
+
+Assuming there are no groups and 'test@bonfacemunyoki.com' does not
+exist in Redis:
+
+.. code-block:: bash
+  python group.py -n "editors" \
+                  -m "me@bonfacemunyoki.com"
+
+results in::
+
+  Successfully created the group: 'editors'
+  `HGET groups 0360449f-5a96-4940-8522-b22d62085da9`: {'name': 'editors', 'admins': [], 'members': ['8ad942fe-490d-453e-bd37-56f252e41603'], 'changed_timestamp': 'Oct 19 2021 09:34AM', 'created_timestamp': 'Oct 19 2021 09:34AM'}
+  
+
+Assuming we have a group's unique id:
+
+.. code-block:: bash
+  python group.py -n "editors" \
+                  -m "me@bonfacemunyoki.com" \
+                  -g "8ad942fe-490d-453e-bd37-56f252e41603"
+
+now results in::
+
+  Successfully created the group: 'editors'
+  `HGET groups 8ad942fe-490d-453e-bd37-56f252e41603`: {'name': 'editors', 'admins': [], 'members': ['8ad942fe-490d-453e-bd37-56f252e41603'], 'changed_timestamp': 'Oct 19 2021 09:38AM', 'created_timestamp': 'Oct 19 2021 09:38AM'}
+  
+If 'me@bonfacemunyoki.com' exists in 'users' in Redis for the above
+command and we run:
+
+.. code-block:: bash
+  python group.py -n "editors" \
+                  -m "me@bonfacemunyoki.com" \
+                  -g "8ad942fe-490d-453e-bd37-56f252e41603"
+
+now results in::
+
+  No new group was created.
+  `HGET groups 8ad942fe-490d-453e-bd37-56f252e41603`: {'name': 'editors', 'admins': [], 'members': ['8ad942fe-490d-453e-bd37-56f252e41603'], 'changed_timestamp': 'Oct 19 2021 09:40AM'}
+
+
+"""
+
+import argparse
+import datetime
+import redis
+import json
+import uuid
+
+from typing import Dict, Optional, Set
+
+
+def create_group_data(users: Dict, target_group: str,
+                      members: Optional[str] = None,
+                      admins: Optional[str] = None,
+                      group_id: Optional[str] = None) -> Dict:
+    """Create group data which is isomorphic to a redis HSET i.e.: KEY,
+    FIELD and VALUE.  If the group_id is not specified, a unique hash
+    will be generated.
+
+    The "field" return value is a unique-id that is used to
+    distinguish the groups.
+
+    Args:
+      - users: a list of users for example:
+      {'8ad942fe-490d-453e-bd37-56f252e41603':
+      '{"email_address": "me@test.com",
+        "full_name": "John Doe",
+        "organization": "Genenetwork",
+        "password": {"algorithm": "pbkdf2",
+                     "hashfunc": "sha256",
+                      "salt": "gJrd1HnPSSCmzB5veMPaVk2ozzDlS1Z7Ggcyl1+pciA=",
+                      "iterations": 100000, "keylength": 32,
+                      "created_timestamp": "2021-09-22T11:32:44.971912",
+                      "password": "edcdaa60e84526c6"},
+                      "user_id": "8ad942fe", "confirmed": 1,
+                      "registration_info": {
+                          "timestamp": "2021-09-22T11:32:45.028833",
+                          "ip_address": "127.0.0.1",
+                          "user_agent": "Mozilla/5.0"}}'}
+
+      - target_group: the group name that will be stored inside the
+        "groups" hash in Redis.
+      - members: an optional comma-separated list of values that
+        contain members of the `target_group` e.g. "me@test1.com,
+        me@test2.com, me@test3.com"
+      - admins: an optional comma-separated list of values that
+        contain administrators of the `target_group`
+        e.g. "me@test1.com, me@test2.com, me@test3.com"
+      - group_id: an optional unique identifier for a group. If not
+        set, a unique value will be auto-generated.
+
+    Returns:
+      A dictionary that contains the following keys: "key", "field",
+    and "value" that can be used in a redis hash as follows: HSET key
+    field value
+
+    """
+    # Emails
+    _members: Set = set("".join(members.split()).split(",")
+                        if members else [])
+    _admins: Set = set("".join(admins.split()).split(",")
+                       if admins else [])
+
+    # Unique IDs
+    member_ids: Set = set()
+    admin_ids: Set = set()
+
+    for user_id, user_details in users.items():
+        _details = json.loads(user_details)
+        if _details.get("email_address") in _members:
+            member_ids.add(user_id)
+        if _details.get("email_address") in _admins:
+            admin_ids.add(user_id)
+
+    timestamp: str = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+    return {"key": "groups",
+            "field": (group_id or str(uuid.uuid4())),
+            "value": json.dumps({
+                "name": target_group,
+                "admins": list(admin_ids),
+                "members": list(member_ids),
+                "changed_timestamp": timestamp,
+            })}
+
+
+if __name__ == "__main__":
+    # Initialising the parser CLI arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-n", "--group-name",
+                        help="This is the name of the GROUP mask")
+    parser.add_argument("-g", "--group-id",
+                        help="[Optional] This is the name of the GROUP mask")
+    parser.add_argument("-m", "--members",
+                        help="Members of the GROUP mask")
+    parser.add_argument("-a", "--admins",
+                        help="Admins of the GROUP mask")
+    args = parser.parse_args()
+
+    if not args.group_name:
+        exit("\nExiting. Please specify a group name to use!\n")
+
+    members = args.members if args.members else None
+    admins = args.admins if args.admins else None
+
+    REDIS_CONN = redis.Redis(decode_responses=True)
+    USERS = REDIS_CONN.hgetall("users")
+
+    if not any([members, admins]):
+        exit("\nExiting. Please provide a value for "
+             "MEMBERS(-m) or ADMINS(-a)!\n")
+
+    data = create_group_data(
+        users=USERS,
+        target_group=args.group_name,
+        members=members,
+        admins=admins,
+        group_id=args.group_id)
+
+    if not REDIS_CONN.hget("groups", data.get("field")):
+        updated_data = json.loads(data["value"])
+        timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+        updated_data["created_timestamp"] = timestamp
+        data["value"] = json.dumps(updated_data)
+
+    created_p = REDIS_CONN.hset(data.get("key", ""),
+                                data.get("field", ""),
+                                data.get("value", ""))
+    groups = json.loads(REDIS_CONN.hget("groups",
+                                        data.get("field")))  # type: ignore
+    if created_p:
+        exit(f"\nSuccessfully created the group: '{args.group_name}'\n"
+             f"`HGET groups {data.get('field')}`: {groups}\n")
+    exit("\nNo new group was created.\n"
+         f"`HGET groups {data.get('field')}`: {groups}\n")
diff --git a/scripts/authentication/resource.py b/scripts/authentication/resource.py
new file mode 100755
index 00000000..4b8d801a
--- /dev/null
+++ b/scripts/authentication/resource.py
@@ -0,0 +1,106 @@
+#!/usr/bin/env python3
+"""A script that:
+
+- Optionally restores data from a json file.
+
+- By default, without any args provided, adds the group: 'editors' to
+every resource. 'editors' should have the right to edit both metadata
+and data.
+
+- Optionally creates a back-up every time you edit a resource.
+
+
+To restore a back-up:
+
+.. code-block:: python
+   python resource.py --restore <PATH/TO/RESOURCE/BACK-UP/FILE>
+
+To add editors to every resource without creating a back-up:
+
+.. code-block:: python
+   python resource.py
+
+To add editors to every resource while creating a back-up before any
+destructive edits:
+
+.. code-block:: python
+   python resource.py --enable-backup
+
+"""
+import argparse
+import json
+import redis
+import os
+
+from datetime import datetime
+
+
+def recover_hash(name: str, file_path: str, set_function) -> bool:
+    """Recover back-ups using the `set_function`
+
+    Args:
+      - name: Redis hash where `file_path` will be restored
+      - file_path: File path where redis hash is sourced from
+      - set_function: Function used to do the Redis backup for
+        example: HSET
+
+    Returns:
+      A boolean indicating whether the function ran successfully.
+
+    """
+    try:
+        with open(file_path, "r") as f:
+            resources = json.load(f)
+            for resource_id, resource in resources.items():
+                set_function(name=name,
+                             key=resource_id,
+                             value=resource)
+            return True
+    except Exception as e:
+        print(e)
+        return False
+
+
+if __name__ == "__main__":
+    # Initialising the parser CLI arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--group-id",
+                        help="Add the group id to all resources")
+    parser.add_argument("--restore",
+                        help="Restore from a given backup")
+    parser.add_argument("--enable-backup", action="store_true",
+                        help="Create a back up before edits")
+    args = parser.parse_args()
+
+    if not args.group_id:
+        exit("Please specify the group-id!\n")
+    if args.restore:
+        if recover_hash(name="resources",
+                        file_path=args.back_up,
+                        set_function=redis.Redis(decode_responses=True).hset):
+            exit(f"\n Done restoring {args.back_up}!\n")
+        else:
+            exit(f"\n There was an error restoring {args.back_up}!\n")
+
+    REDIS_CONN = redis.Redis(decode_responses=True)
+    RESOURCES = REDIS_CONN.hgetall("resources")
+    BACKUP_DIR = os.path.join(os.getenv("HOME"), "redis")
+    if args.enable_backup:
+        FILENAME = ("resources-"
+                    f"{datetime.now().strftime('%Y-%m-%d-%I:%M:%S-%p')}"
+                    ".json")
+        if not os.path.exists(BACKUP_DIR):
+            os.mkdir(BACKUP_DIR)
+        with open(os.path.join(BACKUP_DIR, FILENAME), "w") as f:
+            json.dump(RESOURCES, f, indent=4)
+        print(f"\nDone backing upto {FILENAME}")
+
+    for resource_id, resource in RESOURCES.items():
+        _resource = json.loads(resource)  # str -> dict conversion
+        _resource["group_masks"] = {args.group_id: {"metadata": "edit",
+                                                    "data": "edit",
+                                                    "admin": "not-admin"}}
+        REDIS_CONN.hset("resources",
+                        resource_id,
+                        json.dumps(_resource))
+    exit("Done updating `resources`\n")